I have read studies that claim high pitch outing and heavy workloads are damaging and increase injury risks, and intuitively this makes sense to us. The major clash comes when developing pitchers. Some may say that front offices should strive to build arm strength early by allowing pitchers to go deep into games. This way that are more accustomed to throwing many pitches in an outing and can improve their endurance. Others, and the Red Sox fall on this side, argue that pitch counts and inning workloads should be strictly monitored so as to not risk future injury.
There is no doubt that the amount of money invested in young pitchers these days may play a role in these debates. I tend to agree pitchers should be monitored closely and progressively allowed to stretch out deeper into games. The one thing to watch for though is previous exposure to high pitch counts. College coaches are notorious for leaving pitchers in the game for far too long. Boyd's World tracks Pitcher Abuse Points each year and you can see some really startling totals.
I have little doubt some pitchers today could go out and throw complete games every time out (Roy Halladay?) but why take the risk. One thing I would stress is that 100 pitches should not be the absolute cut off for every pitcher. There are obviously work-horse types that can last longer than others on a consistent basis. It would be up to the manager to determine when his player was tiring.